New insight into detection and evolution of Australian Penaeus stylirostris densovirus
Jaroenram, Wansadaj (2015) New insight into detection and evolution of Australian Penaeus stylirostris densovirus. PhD thesis, James Cook University.
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Abstract
Penaeus stylirostris densovirus (PstDV) has caused high mortality in Penaeus stylirostris and runt deformity syndrome in Penaeus vannamei and Penaeus monodon. This study aims to 1) develop a practical diagnostic approach to separate infectious PstDV from endogenous viral elements, and 2) to determine the factors that underlie molecular evolution of the Australian PstDV. Regarding the first, we mapped the PstDV insertion patterns in the genome of Australian P. monodon. A detection platform based on recombinase polymerase amplification (RPA) and a lateral flow dipstick (LFD) was developed for detecting PstDV based on the DNA region that is least likely to be endogenized. Under the optimal conditions, 30 min at 37 °C for RPA followed by 5 min at room temperature for LFD, the platform was 10 times more sensitive than the Saksmerphrome et al's interim 3-tube nested PCR and showed no cross-reaction with other shrimp viruses. It also reduced false positive results arising from viral inserts to ~5% compared to 76–78% by the IQ2000™ nested PCR kit and the 309F/R PCR protocol currently recommended by World Organization for Animal Health for PstDV detection. Together with simplicity and portability, the protocol serves as an alternative tool to PCR for screening PstDV.
As for the second objective, A 1-bp deletion (1305delA) within the nuclear localization signal-encoding sequence of open reading frame 1 (ORF1; NS1) of Australian PstDV was identified as a cause of 199-amino acid shortened NS1 protein and production of a second protein, C-terminal NS1. This mutation is believed to reduce virulence as it strongly modifies the characteristics of NS1, which is responsible for the majority of enzymatic activities in PstDV. This finding supports a hypothesis regarding accommodation of PstDV in Australian prawns in relation to viral genetics. However, a high degree of evolution (1.55 × 10⁻³ substitutions/site/year) for the virus, which was attributable to the viral recombination, was observed with 10 potential genomic breakpoints identified. With this finding, we suggest that awareness of the emergence of new virulent strains should be increased as a preventative measure against future outbreaks of PstDV in the Australian Indo-Pacific.
| Item ID: | 41272 |
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| Item Type: | Thesis (PhD) |
| Keywords: | blue shrimp; detection; IHHNV; LFD; Penaeus stylirostris densovirus; Penaeus stylirostris; point mutation; prawns; PstDV; PstDV-related sequences; recombinase polymerase amplification; RPA; shrimps; viral accommodation; viral Evolution; viral genetics; virology |
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| Additional Information: | Publications arising from this thesis are available from the Related URLs field. The publications are: Jaroenram, Wansadaj, Chaivisuthangkura, Parin, and Owens, Leigh (2015) One base pair deletion and high rate of evolution: keys to viral accommodation of Australian Penaeus stylirostris densovirus. Aquaculture, 443. pp. 40-48. Jaroenram, Wansadaj, and Owens, Leigh (2014) Recombinase polymerase amplification combined with a lateral flow dipstick for discriminating between infectious Penaeus stylirostris densovirus and virus-related sequences in shrimp genome. Journal of Virological Methods, 208. pp. 144-151. Jaroenram, Wansadaj, and Owens, Leigh (2014) Separation of endogenous viral elements from infectious Penaeus stylirostris densovirus using recombinase polymerase amplification. Molecular and Cellular Probes, 28 (5-6). pp. 284-287. |
| Date Deposited: | 01 Dec 2015 06:26 |
| FoR Codes: | 06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060506 Virology @ 50% 07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070404 Fish Pests and Diseases @ 50% |
| SEO Codes: | 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830105 Aquaculture Prawns @ 100% |
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